User.findOneByEmail - like mongooses findOne except the first arg is an email_address instead of a condition
User.findByEmail - same here... this is useful if unique is set to false and more than one doc has the same email
User.findByEmailVerificationCode - find the doc by one of it's email verification codes
User.emailExists - use this to check if email exists within entire collection so you can quickly throw that "email already exists" error on your signup forms or something with that cool new API

Empower your self with easy methods on the instance...

user.getPrimaryEmail // returns the email object
user.setPrimaryEmail // sets email_address as primary and removes primary from the other email object
user.findEmail // find the email object within the doc
user.removeEmail // removes and saves the doc with the loss of an email address
user.emailExists // do we have the email in the doc? It's always a yes or no answer
user.isPrimaryEmail // is it?
user.startEmailVerificationProcess // this configures and saves some stuff like a verification code and expiration date for that verification code
user.getEmailByVerificationCode // if you don't have the doc in memory find it first with the static: findByEmailVerificationCode
user.verifyEmail // verify that email
user.isVerifiedEmail // returns boolean on rather or not that email address has been verified

Use the one and only extremely powerful virtual field that hands down that primary email address at all times unless it's undefined

user.email; // the primary email or equivalent of user.getPrimaryEmail().email_address

Misc Notes

On creation/save the first email will become primary pre save if there is not a current primary email address unless there are no email addresses.